selected scholarly activity
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academic article
- Modifiable factors related to life-space mobility in community-dwelling older adults: results from the Canadian Longitudinal Study on Aging. BMC Geriatrics. 20:35. 2020
- Reconciling early-outbreak estimates of the basic reproductive number and its uncertainty: framework and applications to the novel coronavirus (SARS-CoV-2) outbreak. Journal of the Royal Society Interface. 17:20200144-20200144. 2020
- Inferring generation-interval distributions from contact-tracing data. Journal of the Royal Society Interface. 17:20190719-20190719. 2020
- Modeling shield immunity to reduce COVID-19 epidemic spread. Nature Medicine. 26:849-854. 2020
- The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak. Epidemics. 31:100392-100392. 2020
- Moving Beyond a Peak Mentality: Plateaus, Shoulders, Oscillations and Other 'Anomalous' Behavior-Driven Shapes in COVID-19 Outbreaks. medRxiv. 2020
- Calibration of individual-based models to epidemiological data: A systematic review. PLoS Computational Biology. 16:e1007893-e1007893. 2020
- The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak. medRxiv. 2020
- Traditional Male Circumcision is Associated with Sexual Risk Behaviors in Sub-Saharan Countries Prioritized for Male Circumcision. AIDS and Behavior. 24:951-959. 2020
- Patterns of seasonal and pandemic influenza-associated health care and mortality in Ontario, Canada. BMC Public Health. 19:1237. 2019
- Inferring generation-interval distributions from contact-tracing data 2019
- A practical generation-interval-based approach to inferring the strength of epidemics from their speed. Epidemics. 27:12-18. 2019
- I can see clearly now: Reinterpreting statistical significance. Methods in Ecology and Evolution. 10:756-759. 2019
- Correction: Male and female bees show large differences in floral preference. PLoS ONE. 14:e0217714-e0217714. 2019
- Male and female bees show large differences in floral preference. PLoS ONE. 14:e0214909-e0214909. 2019
- Couple serostatus patterns in sub-Saharan Africa illuminate the relative roles of transmission rates and sexual network characteristics in HIV epidemiology. Scientific Reports. 8:6675. 2018
- Partner age differences and associated sexual risk behaviours among adolescent girls and young women in a cash transfer programme for schooling in Malawi. BMC Public Health. 18:403. 2018
- Male and female bees show large differences in floral preference 2018
- Healthcare Resource Uses and Out-of-Pocket Expenses Associated with Pulmonary TB Treatment in Thailand. PharmacoEconomics - Open. 2:297-308. 2018
- Out-of-Pocket Expenditures, Indirect Costs and Health-Related Quality of Life of Patients with Pulmonary Tuberculosis in Thailand. PharmacoEconomics - Open. 2:281-296. 2018
- Human ectoparasite transmission of the plague during the Second Pandemic is only weakly supported by proposed mathematical models. Proceedings of the National Academy of Sciences of the United States of America. 115:E7892-E7893. 2018
- Fitting mechanistic epidemic models to data: A comparison of simple Markov chain Monte Carlo approaches. Statistical Methods in Medical Research. 27:1956-1967. 2018
- Correction to ‘Speciation over the edge: gene flow among non-human primate species across a formidable biogeographic barrier’. Royal Society Open Science. 5:180736-180736. 2018
- Equivalence of the Erlang Seir Epidemic Model and the Renewal Equation 2018
- Stochastic simulation of multiscale complex systems with PISKaS: A rule-based approach. Biochemical and Biophysical Research Communications. 498:342-351. 2018
- Two approaches to forecast Ebola synthetic epidemics. Epidemics. 22:36-42. 2018
- On the origin of obesity: identifying the biological, environmental and cultural drivers of genetic risk among human populations. Obesity Reviews. 19:121-149. 2018
- Equivalence of the Erlang-Distributed SEIR Epidemic Model and the Renewal Equation. SIAM Journal on Applied Mathematics. 78:3258-3278. 2018
- Relatedness of the incidence decay with exponential adjustment (IDEA) model, “Farr's law” and SIR compartmental difference equation models. Infectious Disease Modelling. 3:1-12. 2018
- Patterns of influenza vaccination coverage in the United States from 2009 to 2015. International Journal of Infectious Diseases. 65:122-127. 2017
- Kaiso is highly expressed in TNBC tissues of women of African ancestry compared to Caucasian women. Cancer Causes and Control. 28:1295-1304. 2017
- Speciation over the edge: gene flow among non-human primate species across a formidable biogeographic barrier. Royal Society Open Science. 4:170351-170351. 2017
- Quantifying ethical tradeoffs for vaccine efficacy trials during severe epidemics 2017
- Lysis, lysogeny and virus–microbe ratios. Nature Nature: New biology. 549:E1-E3. 2017
- A double-edged sword: does highly active antiretroviral therapy contribute to syphilis incidence by impairing immunity toTreponema pallidum?. Sexually Transmitted Infections. 93:374-378. 2017
- Eco-Evolutionary Theory and Insect Outbreaks. American Naturalist. 189:616-629. 2017
- Role of pharmaceutical care for self-administered pulmonary tuberculosis treatment in Thailand. Journal of Clinical Pharmacy and Therapeutics. 42:337-344. 2017
- Fitting mechanistic epidemic models to data: a comparison of simple Markov chain Monte Carlo approaches 2017
- Evidence that promotion of male circumcision did not lead to sexual risk compensation in prioritized Sub-Saharan countries. PLoS ONE. 12:e0175928-e0175928. 2017
- Epidemiological impact of a syphilis vaccine: a simulation study. Epidemiology and Infection. 144:3244-3252. 2016
- Stochasticity and the limits to confidence when estimating R0 of Ebola and other emerging infectious diseases. Journal of Theoretical Biology. 408:145-154. 2016
- Reevaluating Cumulative HIV-1 Viral Load as a Prognostic Predictor: Predicting Opportunistic Infection Incidence and Mortality in a Ugandan Cohort. American Journal of Epidemiology. 184:67-77. 2016
- The Hayflick Limit May Determine the Effective Clonal Diversity of Naive T Cells. Journal of Immunology. 196:4999-5004. 2016
- Estimating finite-population reproductive numbers in heterogeneous populations. Journal of Theoretical Biology. 397:1-12. 2016
- Lytic to temperate switching of viral communities. Nature Nature: New biology. 531:466-470. 2016
- The risk of incomplete personal protection coverage in vector-borne disease. Journal of the Royal Society Interface. 13:20150666-20150666. 2016
- Bifurcations and Chaotic Dynamics in a Tumour-Immune-Virus System. Mathematical Modelling of Natural Phenomena. 11:65-85. 2016
- Intrinsic and realized generation intervals in infectious-disease transmission. Proceedings of the Royal Society B: Biological Sciences. 282:20152026-20152026. 2015
- The effect of sexually transmitted co-infections on HIV viral load amongst individuals on antiretroviral therapy: a systematic review and meta-analysis. BMC Infectious Diseases. 15:249. 2015
- Evaluating Ebola vaccine trials: insights from simulation. The Lancet Infectious Diseases. 15:1134-1134. 2015
- Modeling the effect of HIV coinfection on clearance and sustained virologic response during treatment for hepatitis C virus. Epidemics. 12:1-10. 2015
- Modeling Post-death Transmission of Ebola: Challenges for Inference and Opportunities for Control. Scientific Reports. 5:8751. 2015
- Statistical power and validity of Ebola vaccine trials in Sierra Leone: a simulation study of trial design and analysis. The Lancet Infectious Diseases. 15:703-710. 2015
- Correction: Estimating the Global Burden of Endemic Canine Rabies. PLoS Neglected Tropical Diseases. 9:e0003786-e0003786. 2015
- Estimating the Global Burden of Endemic Canine Rabies. PLoS Neglected Tropical Diseases. 9:e0003709-e0003709. 2015
- Reassessment of HIV-1 Acute Phase Infectivity: Accounting for Heterogeneity and Study Design with Simulated Cohorts. PLoS Medicine. 12:e1001801-e1001801. 2015
- Modelling of OGTT curve identifies 1 h plasma glucose level as a strong predictor of incident type 2 diabetes: results from two prospective cohorts. Diabetologia. 58:87-97. 2015
- Ebola virus vaccine trials: the ethical mandate for a therapeutic safety net. British Medical Journal BMJ (Clinical research ed.). 349:g7518-g7518. 2014
- Ebola control: effect of asymptomatic infection and acquired immunity. The Lancet. 384:1499-1500. 2014
- Analytic Calculation of Finite-Population Reproductive Numbers for Direct- and Vector-Transmitted Diseases with Homogeneous Mixing. Bulletin of Mathematical Biology. 76:1143-1154. 2014
- Species Abundance, Not Diet Breadth, Drives the Persistence of the Most Linked Pollinators as Plant-Pollinator Networks Disassemble. American Naturalist. 183:600-611. 2014
- Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm. FEMS Microbiology Ecology. 87:403-415. 2014
- Re: "The 'Case-Chaos Study' l Adjunct or Alternative to Conventional Case-Control Study Methodology". American Journal of Epidemiology. 179:261-262. 2014
- Estimating Initial Epidemic Growth Rates. Bulletin of Mathematical Biology. 76:245-260. 2014
- Intimate partner violence is associated with HIV infection in women in Kenya: A cross-sectional analysis. BMC Public Health. 13:512. 2013
- Population-level effects of clinical immunity to malaria. BMC Infectious Diseases. 13:428. 2013
- Patterns of spread of influenza A in Canada. Proceedings of the Royal Society B: Biological Sciences. 280:20131174-20131174. 2013
- Inferring the causes of the three waves of the 1918 influenza pandemic in England and Wales. Proceedings of the Royal Society B: Biological Sciences. 280:20131345-20131345. 2013
- Effects of mixing in threshold models of social behavior. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 88:012816. 2013
- Robust estimation of microbial diversity in theory and in practice. ISME Journal. 7:1092-1101. 2013
- Extra-couple HIV transmission in sub-Saharan Africa: a mathematical modelling study of survey data. The Lancet. 381:1561-1569. 2013
- Genomic Dynamics of Transposable Elements in the Western Clawed Frog (Silurana tropicalis). Genome Biology and Evolution. 5:998-1009. 2013
- Designing Programs for Eliminating Canine Rabies from Islands: Bali, Indonesia as a Case Study. PLoS Neglected Tropical Diseases. 7:e2372-e2372. 2013
- HIV Sexual Transmission Is Predominantly Driven by Single Individuals Rather than Discordant Couples: A Model-Based Approach. PLoS ONE. 8:e82906-e82906. 2013
- A non-negative matrix factorization framework for identifying modular patterns in metagenomic profile data. Journal of Mathematical Biology. 64:697-711. 2012
- Effects of School Closure on Incidence of Pandemic Influenza in Alberta, Canada. Annals of Internal Medicine. 156:173-173. 2012
- Agricultural intensification, priming for persistence and the emergence of Nipah virus: a lethal bat-borne zoonosis. Journal of the Royal Society Interface. 9:89-101. 2012
- Functional Biogeography of Ocean Microbes Revealed through Non-Negative Matrix Factorization. PLoS ONE. 7:e43866-e43866. 2012
- How to Make Epidemiological Training Infectious. PLoS Biology. 10:e1001295-e1001295. 2012
- Multi-Stability and Multi-Instability Phenomena in a Mathematical Model of Tumor-Immune-Virus Interactions. Bulletin of Mathematical Biology. 73:2932-2961. 2011
- The odds of duplicate gene persistence after polyploidization. BMC Genomics. 12:599. 2011
- Age-specific mortality risk from pandemic influenza. Journal of Theoretical Biology. 288:29-34. 2011
- Mechanistic modelling of the three waves of the 1918 influenza pandemic. Theoretical Ecology. 4:283-288. 2011
- Prevalence of Epistasis in the Evolution of Influenza A Surface Proteins. PLoS Genetics. 7:e1001301-e1001301. 2011
- Modeling the Population-Level Effects of Male Circumcision as an HIV-Preventive Measure: A Gendered Perspective. PLoS ONE. 6:e28608-e28608. 2011
- Unlocking the forest inventory data: relating individual tree performance to unmeasured environmental factors. Ecological Applications. 20:684-699. 2010
- Fluctuation domains in adaptive evolution. Theoretical Population Biology. 77:6-13. 2010
- Reconstructing influenza incidence by deconvolution of daily mortality time series. Proceedings of the National Academy of Sciences of the United States of America. 106:21825-21829. 2009
- Unsupervised statistical clustering of environmental shotgun sequences. BMC Bioinformatics. 10:316. 2009
- Initial human transmission dynamics of the pandemic (H1N1) 2009 virus in North America. Influenza and other Respiratory Viruses. 3:215-222. 2009
- Directionality in the evolution of influenza A haemagglutinin. Proceedings of the Royal Society B: Biological Sciences. 276:3035-3035. 2009
- On the Accessibility of Adaptive Phenotypes of a Bacterial Metabolic Network. PLoS Computational Biology. 5:e1000472-e1000472. 2009
- Avoiding spurious findings of nonrandom social structure in association data. Animal Behaviour. 77:1381-1385. 2009
- Reproductive status influences group size and persistence of bonds in male plains zebra (Equus burchelli). Behavioral Ecology and Sociobiology. 63:1035-1043. 2009
- On the use of hemagglutination-inhibition for influenza surveillance: Surveillance data are predictive of influenza vaccine effectiveness. Vaccine. 27:2447-2452. 2009
- Transmission Dynamics and Prospects for the Elimination of Canine Rabies. PLoS Biology. 7:e1000053-e1000053. 2009
- Ability to Replicate in the Cytoplasm Predicts Zoonotic Transmission of Livestock Viruses. Journal of Infectious Diseases. 199:565-568. 2009
- A mixability theory for the role of sex in evolution. Proceedings of the National Academy of Sciences of the United States of America. 105:19803-19808. 2008
- Host‐Pathogen Interactions, Insect Outbreaks, and Natural Selection for Disease Resistance. American Naturalist. 172:829-842. 2008
- Directionality in the evolution of influenza A haemagglutinin. Proceedings of the Royal Society B: Biological Sciences. 275:2455-2464. 2008
- SCALING FROM TREES TO FORESTS: TRACTABLE MACROSCOPIC EQUATIONS FOR FOREST DYNAMICS. Ecological Monographs. 78:523-545. 2008
- WHITE SPRUCE MEETS BLACK SPRUCE: DISPERSAL, POSTFIRE ESTABLISHMENT, AND GROWTH IN A WARMING CLIMATE. Ecological Monographs. 78:489-505. 2008
- Antibiotic Overuse: The Influence of Social Norms. Journal of the American College of Surgeons. 207:265-275. 2008
- Exploring reservoir dynamics: a case study of rabies in the Serengeti ecosystem. Journal of Applied Ecology. 45:1246-1257. 2008
- Natural Selection for Nucleotide Usage at Synonymous and Nonsynonymous Sites in Influenza A Virus Genes. Journal of Virology. 82:4938-4945. 2008
- Alternative stable states in host–phage dynamics. Theoretical Ecology. 1:13-19. 2008
- Rabies Exposures, Post-Exposure Prophylaxis and Deaths in a Region of Endemic Canine Rabies. PLoS Neglected Tropical Diseases. 2:e339-e339. 2008
- Intraspecific Variation and Species Coexistence. American Naturalist. 170:807-818. 2007
- Native bees provide insurance against ongoing honey bee losses. Ecology Letters. 10:1105-1113. 2007
- On State-Space Reduction in Multi-Strain Pathogen Models, with an Application to Antigenic Drift in Influenza A. PLoS Computational Biology. 3:e159-e159. 2007
- The Genesis and Spread of Reassortment Human Influenza A/H3N2 Viruses Conferring Adamantane Resistance. Molecular Biology and Evolution. 24:1811-1820. 2007
- Synchronous cycles of domestic dog rabies in sub-Saharan Africa and the impact of control efforts. Proceedings of the National Academy of Sciences of the United States of America. 104:7717-7722. 2007
- Vaccinating to Protect a Vulnerable Subpopulation. PLoS Medicine. 4:e174-e174. 2007
- Epidemic Enhancement in Partially Immune Populations. PLoS ONE. 2:e165-e165. 2007
- Network metrics reveal differences in social organization between two fission–fusion species, Grevy’s zebra and onager. Oecologia. 151:140-149. 2007
- Bursts of nonsynonymous substitutions in HIV-1 evolution reveal instances of positive selection at conservative protein sites. Proceedings of the National Academy of Sciences of the United States of America. 103:19396-19401. 2006
- Codon Usage and Selection on Proteins. Journal of Molecular Evolution. 63:635-653. 2006
- Estimating Selection Pressures from Limited Comparative Data. Molecular Biology and Evolution. 23:1457-1459. 2006
- Estimating selection pressures from limited comparative data. Molecular Biology and Evolution. 23:1457-1459. 2006
- Enhancing the Use of Clinical Guidelines: A Social Norms Perspective. Journal of the American College of Surgeons. 202:826-836. 2006
- Battling bad behavior (vol 20, pg 51, 2002). Scientist. 20:15-15. 2006
- Erratum: Battling bad behavior (Scientist 20, 2 (51-57)). Scientist. 20:15. 2006
- A Monte Carlo model for estimating the productivity of a generalist brood parasite across multiple host species. Evolutionary Ecology Research. 8:213-236. 2006
- Battling bad behavior. Scientist. 20:51-+. 2006
- US flu mortality estimates are based on solid science. British Medical Journal BMJ (Clinical research ed.). 332:177.2-178. 2006
- Mortality due to Influenza in the United States—An Annualized Regression Approach Using Multiple-Cause Mortality Data. American Journal of Epidemiology. 163:181-187. 2006
- The entomological inoculation rate and Plasmodium falciparum infection in African children. Nature Nature: New biology. 438:492-495. 2005
- Agricultural Antibiotics and Human Health. PLoS Medicine. 2:e232-e232. 2005
- Directed seed dispersal and metapopulation response to habitat loss and disturbance: application to Eichhornia paniculata. Journal of Ecology. 93:658-669. 2005
- MARINE RESERVE DESIGN AND THE EVOLUTION OF SIZE AT MATURATION IN HARVESTED FISH. Ecological Applications. 15:882-901. 2005
- Testing Simple Indices of Habitat Proximity. American Naturalist. 165:707-717. 2005
- Assessing influenza-related mortality: comment on Zucs et al.. Emerging Themes in Epidemiology. 2:7-7. 2005
- Codon volatility does not detect selection (reply). Nature Nature: New biology. 433:E7-E8. 2005
- Dynamical resonance can account for seasonality of influenza epidemics. Proceedings of the National Academy of Sciences of the United States of America. 101:16915-16916. 2004
- The Risk of a Mosquito-Borne Infectionin a Heterogeneous Environment. PLoS Biology. 2:e368-e368. 2004
- The combined effects of pathogens and predators on insect outbreaks. Nature Nature: New biology. 430:341-345. 2004
- Comment on "Metapopulation Persistence with Age-Dependent Disturbance or Succession". Science The Scientific monthly. 304:684c-684c. 2004
- Correction for Smith et al., Persistent colonization and the spread of antibiotic resistance in nosocomial pathogens: Resistance is a regional problem, PNAS 2004 101:3709-3714. Proceedings of the National Academy of Sciences of the United States of America. 101:5696-5696. 2004
- Erratum: Persistent colonization and the spread of antibiotic resistance in nosocomial pathogens: Resistance is a regional problem (Proceedings of the National Academy of Sciences of the United States of America (March 9, 2004) 101, 10 (3709-3714)). Proceedings of the National Academy of Sciences of the United States of America. 101:5696. 2004
- Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum. Nature Nature: New biology. 428:942-945. 2004
- Mangrove filtration of anthropogenic nutrients in the Rio Coco Solo, Panama. Management of Environmental Quality. 15:131-142. 2004
- Persistent colonization and the spread of antibiotic resistance in nosocomial pathogens: Resistance is a regional problem. Proceedings of the National Academy of Sciences of the United States of America. 101:3709-3714. 2004
- Evolution and persistence of influenza A and other diseases. Mathematical Biosciences. 188:17-28. 2004
- A simulation model of African Anopheles ecology and population dynamics for the analysis of malaria transmission.. Malaria Journal. 3:29-29. 2004
- Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza A virus. Proceedings of the National Academy of Sciences of the United States of America. 100:7152-7157. 2003
- Metapopulations, community assembly, and scale invariance in aspect space. Theoretical Population Biology. 62:329-338. 2002
- Ecology and evolution of the flu. Trends in Ecology and Evolution. 17:334-340. 2002
- Hemagglutinin sequence clusters and the antigenic evolution of influenza A virus. Proceedings of the National Academy of Sciences of the United States of America. 99:6263-6268. 2002
- Community assembly and the emergence of ecosystem pattern. Scientia Marina. 65:171-179. 2001
- EVALUATING THE RISKS OF ENGINEERED VIRUSES: MODELING PATHOGEN COMPETITION. Ecological Applications. 11:1602-1609. 2001
- Phenotypic diversity and ecosystem functioning in changing environments: A theoretical framework. Proceedings of the National Academy of Sciences of the United States of America. 98:11376-11381. 2001
- Community of assembly and the emergence of ecosystem pattern. Scientia Marina. 65:171-179. 2001
- Pathogen‐Driven Outbreaks in Forest Defoliators Revisited: Building Models from Experimental Data. American Naturalist. 156:105-120. 2000
- Carrying Capacity and Demographic Stochasticity: Scaling Behavior of the Stochastic Logistic Model. Theoretical Population Biology. 57:59-65. 2000
- Host Heterogeneity and Disease Endemicity: A Moment-Based Approach. Theoretical Population Biology. 56:325-335. 1999
- Local Frequency Dependence and Global Coexistence. Theoretical Population Biology. 55:270-282. 1999
- Limiting Similarity, Species Packing, and System Stability for Hierarchical Competition‐Colonization Models. American Naturalist. 153:371-383. 1999
- Backwards bifurcations and catastrophe in simple models of fatal diseases. Journal of Mathematical Biology. 36:227-248. 1998
- Incorporating Immunological Ideas in Epidemiological Models. Journal of Theoretical Biology. 180:181-187. 1996
- Line intersect sampling of forest canopy gaps. Forest Science. 42:131-138. 1996
- The effects of population heterogeneity on disease invasion. Mathematical Biosciences. 128:25-40. 1995
- Recent and historic red spruce mortality: Evidence of climatic influencee. Water, Air, and Soil Pollution Water, Air, and Soil Pollution: Focus. 30:319-330. 1986
- Post-death Transmission of Ebola: Challenges for Inference and Opportunities for Control
- Synonymous codon usage and selection on proteins
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chapter
- Finding Attractors on a Folding Energy Landscape. 572-582. 2011
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conference paper
- Identifying enterotype in human microbiome by decomposing probabilistic topics into components. 2012 IEEE International Conference on Bioinformatics and Biomedicine. 445-448. 2012
- Incorporating stochasticity in simple models of disease spread. MODELING PARADIGMS AND ANALYSIS OF DISEASE TRANSMISSION MODELS. 121-133. 2010
- Understanding Nipah virus emergence in peninsular Malaysia: The role of epidemic enhancement in domestic pig populations. American Journal of Tropical Medicine and Hygiene. 273-273. 2007
- Bursts of non-synonymous substitutions in HIV-1 phylogenetic tree reveal instances of positive selection at conservative protein sites. PROCEEDINGS OF THE FIFTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE, VOL 3. 114-+. 2006